Metanil yellow is a food dye that has harmful impacts on different body systems. Scutellarin has antioxidant, antiapoptotic, and anti-inflammatory activities. The aim of the current research was to study the effect of chronic administration of metanil yellow on the cerebellar cortex of rats and to evaluate the protective effect of scutellarin. Forty adult male rats were allocated into four groups: group I acted as control, group II was administrated scutellarin (100 mg/kg/day), group III was administrated metanil yellow (200 mg/kg/day), and group IV was administrated scutellarin and metanil yellow as in group II and group III. The agents were administered via oral gavage for 8 weeks. Metanil yellow induced a significant rise in the malondialdehyde coupled with a significant reduction in the superoxide dismutase and glutathione peroxidase. The Purkinje cells were irregular and shrunken with condensed nuclei. A significant elevation in glial fibrillary acidic protein (GFAP) and cleaved caspase-3 as well as a significant reduction of synaptophysin expression were revealed in comparison with the control group. Interestingly, few changes were noticed in rats given metanil yellow concomitant with scutellarin. In conclusion, scutellarin could protect against metanil yellow-induced alterations in the cerebellar cortex by reducing oxidative stress and minimizing gliosis.